His political career began officially in 1971, when he joined the MDB (known as PMDB since 1979) party. Jefferson remained in MDB until 1979, when he went to the Progressive Party (PP). He left the PP in 1980 and he joined the Brazilian Labour Party (PTB), which his grandfather helped to form in 1945.

In 1993, he was cited in a congressional report which investigated bribery in the congressional budgeting committee as an individual who should be "investigated further". Ultimately his financial assets were deemed compatible with his declared income, though undeclared assets were found.[2]

In 1999, he became leader of the PTB party in the Brazilian Chamber of Deputies. He continued as their leader until 2002. In February 2003, PTB elected him as its National President.

In 2005, Jefferson became involved in a corruption scandal related to the Correios, the Brazilian postal administration. Facing a congressional inquiry related to his actions, Jefferson retaliated by exposing a cash-for-votes scheme, where he claimed congressmen were paid monthly sums to in exchange for votes supporting president Luiz Inácio Lula da Silva, in what became known as the Mensalão scandal. The scandal included dozens of parliamentarians of the government's coalition and two government ministers, among others, resulting in the indictment of forty people by the Supreme Federal Tribunal, for their alleged role in one of the country's biggest corruption scandals in recent years.

He was expelled from Congress on September 14, 2005, stemming from his actions in the Correios scandal.[3] The expulsion bars him from being elected to any public office until 2015.[4]